Introduction In recent years, the transcarotid artery revascularisation (TCAR) with flow reversal technique has been developed to treat carotid artery stenosis. The superiority of TCAR over transfemoral carotid artery stenting has been demonstrated. However, the safety and efficacy of TCAR and carotid endarterectomy remain unclear. This study aims to introduce a protocol for a systematic review and meta-analysis to compare the morbidity and mortality rates between TCAR and carotid endarterectomy in the treatment of atherosclerotic carotid artery stenosis. Methods and analysis This protocol was drafted using the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols statement. Herein, major databases will be searched, including Medline, Web of Science, Embase and the Cochrane Library, and randomised controlled trials and high-quality observational studies will be included. We will screen all studies published from January 2000 to March 2021. Bias risk will be evaluated using the Cochrane Collaboration criteria or Methodological Index for Non-randomised Studies criteria, depending on the study type. Two reviewers will select eligible studies and extract the data independently. The primary outcome will include stroke or death during the perioperative period and follow-up. Subgroup and sensitivity analyses will be performed to explore any potential sources of heterogeneity. Specific results will be described in a narrative form when available eligible studies are insufficient for meta-analysis. Publication bias will be assessed using a funnel plot. Ethics and dissemination This study will summarise and analyse the existing literature; hence, ethics approval will not be required. The final results may be published at a relevant academic conference or in a journal. PROSPERO registration number CRD42020178691.